Chaos and Quantum-Classical Correspondence via Phase Space Distribution Functions

Quantum-classical correspondence in conservative chaotic Hamiltonian systems is examined using a uniform structure measure for quantal and classical phase space distribution functions. The similarities and differences between quantum and classical time-evolving distribution functions are exposed by both analytical and numerical means. The quantum-classical correspondence of low-order statistical moments is also studied. The results shed considerable light on quantum-classical correspondence.Comment: 16 pages, 5 figures, to appear in Physical Review

Genetic diversity of equine herpesvirus 1 isolated from neurological, abortigenic and respiratory disease outbreaks

Equine herpesvirus 1 (EHV-1) causes respiratory disease, abortion, neonatal death and neurological disease in equines and is endemic in most countries. The viral factors that influence EHV-1 disease severity are poorly understood, and this has hampered vaccine development. However, the N752D substitution in the viral DNA polymerase catalytic subunit has been shown statistically to be associated with neurological disease. This has given rise to the term “neuropathic strain,” even though strains lacking the polymorphism have been recovered from cases of neurological disease. To broaden understanding of EHV-1 diversity in the field, 78 EHV-1 strains isolated over a period of 35 years were sequenced. The great majority of isolates originated from the United Kingdom and included in the collection were low passage isolates from respiratory, abortigenic and neurological outbreaks. Phylogenetic analysis of regions spanning 80% of the genome showed that up to 13 viral clades have been circulating in the United Kingdom and that most of these are continuing to circulate. Abortion isolates grouped into nine clades, and neurological isolates grouped into five. Most neurological isolates had the N752D substitution, whereas most abortion isolates did not, although three of the neurological isolates from linked outbreaks had a different polymorphism. Finally, bioinformatic analysis suggested that recombination has occurred between EHV-1 clades, between EHV-1 and equine herpesvirus 4, and between EHV-1 and equine herpesvirus 8

Topological complexity of the relative closure of a semi-Pfaffian couple

Gabrielov introduced the notion of relative closure of a Pfaffian couple as an alternative construction of the o-minimal structure generated by Khovanskii's Pfaffian functions. In this paper, use the notion of format (or complexity) of a Pfaffian couple to derive explicit upper-bounds for the homology of its relative closure. Keywords: Pfaffian functions, fewnomials, o-minimal structures, Betti numbers.Comment: 12 pages, 1 figure. v3: Proofs and bounds have been slightly improve

Characterization of human cytomegalovirus genome diversity in immunocompromised hosts by whole genomic sequencing directly from clinical specimens

Background: Advances in next-generation sequencing (NGS) technologies allow comprehensive studies of genetic diversity over the entire genome of human cytomegalovirus (HCMV), a significant pathogen for immunocompromised individuals. Methods: NGS was performed on target-enriched sequence libraries prepared directly from a variety of clinical specimens (blood, urine, breast-milk, respiratory samples, biopsies and vitreous humor) obtained longitudinally or from different anatomical compartments from 20 HCMV-infected patients (renal transplant recipients, stem cell transplant recipients and congenitally infected children). Results: De novo assembled HCMV genome sequences were obtained for 57/68 sequenced samples. Analysis of longitudinal or compartmental HCMV diversity revealed various patterns: no major differences were detected among longitudinal, intra-individual blood samples from 9/15 patients and in most of the patients with compartmental samples, whereas a switch of the major HCMV population was observed in six individuals with sequential blood samples and upon compartmental analysis of one patient with HCMV retinitis. Variant analysis revealed additional aspects of minor virus population dynamics and antiviral resistance mutations. Conclusions: In immunosuppressed patients, HCMV can remain relatively stable or undergo drastic genomic changes that are suggestive of the emergence of minor resident strains or de novo infection

Upper and Lower Bounds on Sizes of Finite Bisimulations of Pfaffian Dynamical Systems

In this paper we study a class of dynamical systems defined by Pfaffian maps. It is a sub-class of o-minimal dynamical systems which capture rich continuous dynamics and yet can be studied using finite bisimulations. The existence of finite bisimulations for o-minimal dynamical and hybrid systems has been shown by several authors; see e.g. Brihaye et al (2004), Davoren (1999), Lafferriere et al (2000). The next natural question to investigate is how the sizes of such bisimulations can be bounded. The first step in this direction was done by Korovina et al (2004) where a double exponential upper bound was shown for Pfaffian dynamical and hybrid systems. In the present paper we improve this bound to a single exponential upper bound. Moreover we show that this bound is tight in general, by exhibiting a parameterized class of systems on which the exponential bound is attained. The bounds provide a basis for designing efficient algorithms for computing bisimulations, solving reachability and motion planning problems

Generalized quantum Fokker-Planck, diffusion and Smoluchowski equations with true probability distribution functions

Traditionally, the quantum Brownian motion is described by Fokker-Planck or diffusion equations in terms of quasi-probability distribution functions, e.g., Wigner functions. These often become singular or negative in the full quantum regime. In this paper a simple approach to non-Markovian theory of quantum Brownian motion using {\it true probability distribution functions} is presented. Based on an initial coherent state representation of the bath oscillators and an equilibrium canonical distribution of the quantum mechanical mean values of their co-ordinates and momenta we derive a generalized quantum Langevin equation in $c$-numbers and show that the latter is amenable to a theoretical analysis in terms of the classical theory of non-Markovian dynamics. The corresponding Fokker-Planck, diffusion and the Smoluchowski equations are the {\it exact} quantum analogues of their classical counterparts. The present work is {\it independent} of path integral techniques. The theory as developed here is a natural extension of its classical version and is valid for arbitrary temperature and friction (Smoluchowski equation being considered in the overdamped limit).Comment: RevTex, 16 pages, 7 figures, To appear in Physical Review E (minor revision